Add pre-commit code checks (#145)

* Add pre-commit code checks
* Remove self-qualification
* Cleanup some used function from packages
* Update codechecks
* Apply formatter
* Add JuliaFormatter to CI
* Fix EOF
* Fix trailing WS
* Format test and Use correct function from ExplicitImports
* Fix some faulty formatting actions
* Update deps

Author: termi-official

.JuliaFormatter.toml

@@ -0,0 +1,7 @@
+style = "sciml"
+align_assignment = true
+margin = 100
+remove_extra_newlines = false
+whitespace_in_kwargs = true
+whitespace_typedefs = true
+ignore = ["bak/*", "benchmarks/*", "data/*", "docs/*"]

.github/workflows/TagBot.yml

@@ -12,4 +12,4 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/codechecks.yaml

@@ -0,0 +1,42 @@
+name: Code checks
+
+on:
+  pull_request:
+  push:
+    branches: ["main"]
+
+jobs:
+
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
+
+  format:
+    runs-on: ubuntu-latest
+    name: "JuliaFormatter.jl"
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.12'
+
+      - uses: actions/checkout@v6
+      - name: Install JuliaFormatter and format
+        # This will use the latest version by default but you can set the version like so:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
+        run: |
+          julia -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter")); Pkg.Apps.add(PackageSpec(name="JuliaFormatter"))'
+          $HOME/.julia/bin/jlfmt --inplace -v .
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+repos:
+  - repo: 'https://github.com/pre-commit/pre-commit-hooks'
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace

Project.toml

@@ -11,7 +11,6 @@ FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
 Ferrite = "c061ca5d-56c9-439f-9c0e-210fe06d3992"
 FerriteGmsh = "4f95f4f8-b27c-4ae5-9a39-ea55e634e36b"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
-GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -29,6 +28,7 @@ SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SparseMatricesCSR = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
 Tensors = "48a634ad-e948-5137-8d70-aa71f2a747f4"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
@@ -62,6 +62,7 @@ OrdinaryDiffEqOperatorSplitting = "0.2.3"
 OrdinaryDiffEqTsit5 = "1"
 Preferences = "1"
 SciMLBase = "2"
+SymbolicIndexingInterface = "0.3.46"
 UnPack = "1"
 julia = "1.10"
 

README.md

@@ -12,7 +12,7 @@ A modular shared-memory high-performance framework for multiscale cardiac multip
 > This package is under heavy development. Expect regular breaking changes
 > for now. If you are interested in joining development, then either comment
 > an issue you are interested or directly reach out to me via julialang.zulipchat.com, mail or
-> julialang.slack.com. Alternatively open a [GitHub discussion](https://github.com/JuliaHealth/Thunderbolt.jl/discussions) if you have something 
+> julialang.slack.com. Alternatively open a [GitHub discussion](https://github.com/JuliaHealth/Thunderbolt.jl/discussions) if you have something
 > specific in mind.
 
 ## Questions
@@ -46,7 +46,7 @@ You are now all set to start using Thunderbolt!
 ## Accessing the Documentation Offline
 
 To build the docs you first need to install Julia, see <https://julialang.org/> for details.
-Then you need to install the packages. To accomplish this you first start a julia shell in the 
+Then you need to install the packages. To accomplish this you first start a julia shell in the
 docs fonder and open the Pkg REPL; i.e. press `]` at the `julia>` promp to
 enter `pkg>` mode. Then you [activate and instantiate](https://pkgdocs.julialang.org/v1/environments/#Using-someone-else's-project) via
 ```

bak/examples-gpu/spiral-wave.jl

@@ -91,7 +91,7 @@ spiral_wave_initializer!(u₀, odeform)
 u₀gpu = CuVector(u₀)
 problem = OS.OperatorSplittingProblem(odeform, u₀gpu, tspan)
 
-# 
+#
 function BJPprec(A,p)
     P = BlockJacobiPreconditioner(A, 1000, CUDABackend())
     KrylovPreconditioners.update!(P, A)

bak/examples/isolated-lumped-circuit.jl

@@ -60,7 +60,7 @@ pt0sat = 100.0
 qt0sat = 0.0
 ## Systemic Arteriole #### Checked
 Rsar = 0.5
-## Systemic Capillary #### Checked 
+## Systemic Capillary #### Checked
 Rscp = 0.52
 ## Systemic Vein #### Checked
 Csvn = 20.5
@@ -97,7 +97,7 @@ Kf_sav = 0.0004
 Ke_sav = 9000.0
 M_sav = 0.0004
 A_sav = 0.00047
-# right heart # 
+# right heart #
 Kst_ra = 2.5
 Kst_rv = 20.0
 Kf_pav = 0.0004
@@ -109,7 +109,7 @@ A_pav = 0.00047
 Kp_av = 5500.0 # *  57.29578 # Shi Paper has values in radians!
 Kf_av = 50.0
 Kf_mv = 50.0
-Kp_mv = 5500.0 # *  57.29578 
+Kp_mv = 5500.0 # *  57.29578
 Kf_tv = 50.0
 Kp_tv = 5500.0 # *  57.29578
 Kf_pv = 50.0
@@ -131,7 +131,7 @@ Kv_pv = 3.5
 θmin_pv = 5.0 * pi / 180
 θmin_tv = 5.0 * pi / 180
 
-## pressure force and frictional force is the same for all 4 valves 
+## pressure force and frictional force is the same for all 4 valves
 
 # Initial conditions #### Checked against cellML model
 

bak/examples/leads.jl

@@ -13,10 +13,10 @@ ms = OrthotropicMicrostructureModel(
 )
 
 κ = SpectralTensorCoefficient(
-    ms, 
+    ms,
     ConstantCoefficient(SVector(0.3, 0.12, 0.12) + SVector(0.3, 0.03, 0.03)))
 κᵢ = SpectralTensorCoefficient(
-    ms, 
+    ms,
     ConstantCoefficient(SVector(0.3, 0.12, 0.12)))
 
 

benchmarks/benchmarks-cuda-linear-form.jl

@@ -1,8 +1,8 @@
 using BenchmarkTools, Thunderbolt, StaticArrays,Ferrite , CUDA
 
 # The Following is needed to enforce grid to use Float32.
-left = Vec((-1.f0, -1.f0,-1.f0)) 
-right = Vec((1.f0, 1.f0, 1.f0)) 
+left = Vec((-1.f0, -1.f0,-1.f0))
+right = Vec((1.f0, 1.f0, 1.f0))
 
 grid = generate_grid(Hexahedron , (500,100,100),left,right)